Contacts of the helix formed by residues 224 - 229 (chain B) in PDB entry 1H8F
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 224 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B CYS* 5.0 0.2 - - - -
222B TYR 3.5 3.2 + - - -
223B ARG* 1.3 75.6 - - - +
225B PRO* 1.3 76.5 - - + +
226B GLU* 3.6 20.2 - - + +
227B LEU* 2.8 24.5 + - + +
228B ILE* 3.1 5.8 + - - +
238B ILE* 4.2 20.4 + - + +
241B TRP* 3.4 25.6 - - + -
328B ARG* 4.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ARG 3.9 0.6 - - - -
224B ALA* 1.3 86.5 - - + +
226B GLU* 1.3 69.5 + - - +
228B ILE* 2.9 25.7 + - + +
229B PHE* 2.9 25.0 + - + -
241B TRP* 3.5 44.9 - - + -
266B LEU* 5.0 3.1 - - + -
269B ILE* 4.4 7.2 - - + -
284B MET* 3.5 22.7 - - - -
323B TYR* 4.4 13.9 - - + -
328B ARG* 3.9 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ALA* 3.6 11.7 - - - +
225B PRO* 1.3 75.3 - - - +
227B LEU* 1.3 60.0 + - - +
229B PHE* 3.4 4.6 + - - +
230B GLY 3.3 3.1 + - - -
231B ALA* 2.8 33.8 + - + +
234B TYR* 4.1 15.2 - - + +
235B THR 5.4 0.5 + - - -
237B SER* 4.0 2.1 + - - -
238B ILE* 3.7 21.5 - - + +
284B MET* 3.3 36.2 - - - +
323B TYR 4.5 1.7 - - - +
325B PRO* 3.4 19.4 - - + +
328B ARG* 2.8 43.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B SER* 4.0 12.0 - - - +
217B ILE* 4.0 7.0 - - + +
218B CYS* 3.7 33.4 - - + -
223B ARG* 3.4 30.1 + - + +
224B ALA 2.8 27.8 + - - +
226B GLU* 1.3 78.0 - - - +
228B ILE* 1.3 64.6 + - - +
230B GLY* 2.9 14.6 + - - -
231B ALA 4.7 2.9 - - - +
234B TYR* 3.7 36.6 - - + -
238B ILE* 3.8 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A SER* 5.2 2.3 + - - -
216A TYR* 3.4 32.0 + - + +
223B ARG* 4.0 30.8 + - + +
224B ALA 3.1 10.3 + - - +
225B PRO* 2.9 9.4 + - + +
227B LEU* 1.3 76.5 - - - +
229B PHE* 1.3 58.9 + - - +
230B GLY* 3.1 4.0 + - - -
262B GLY* 3.8 17.7 - - - +
265B GLN* 3.9 26.5 - - + +
266B LEU* 3.5 37.7 - - + -
269B ILE* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A SER* 5.4 0.2 - - - -
216A TYR* 3.8 20.9 - + - -
225B PRO* 2.9 29.6 + - + +
226B GLU* 3.9 3.1 - - - +
227B LEU 3.2 0.2 - - - -
228B ILE* 1.3 75.0 - - + +
230B GLY* 1.3 58.4 + - - +
231B ALA 3.3 0.7 - - - -
266B LEU* 3.7 25.4 - - + -
276B PRO* 5.6 3.6 - - + -
281B ILE* 5.1 8.5 - - + -
284B MET* 3.7 39.0 - - + -
286B PRO* 2.8 41.8 - - + +
288B TYR* 3.5 29.9 - + + -
291B PHE* 3.5 41.1 - + - -
323B TYR* 5.9 1.6 - + - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il